Using a combination of UHV-STM and molecular mechanics calculations, we investigate the surface self-assembly of a complex multi-component metal-molecule system with synergistic non-covalent interactions. Hydrogen bonding between three-dimensional Lander-DAT molecules and planar PTCDI molecules, adsorbed closer to the surface, is found to be facilitated by electrostatic interactions between co-adsorbed Ni adatoms and the flexible molecular DAT groups.

The coating effect of a graphene layer on the reconstructed Pt(100) surface toward reactive gases is investigated by a combination of scanning tunneling microscopy experiments and density functional theory calculations. We observe that while the graphene coating is effective toward individual exposures of O-2 and H2S, a sequential dose of O-2 and H2S causes a breakdown of the coating effect. From density functional theory calculations we explain these observations at the atomic level. We show that it is favorable for oxygen atoms to disrupt the Pt-C bonds at the graphene edge to insert between the edge and the surface in a bridging position. This closed-edge configuration explains why oxygen alone is not found to intercalate under the graphene at room temperature. With the subsequent dosing of H2S, we propose that the oxygen atoms are released from the platinum surface causing the breakdown of the coating effect.

The atomic-scale identification of the G4K1 structural motif is achieved using an interplay of STM imaging and DFT calculations. Its high stability is found to be caused by the delicate balance between hydrogen bonding and metal-ligand interaction, which is of utmost relevance to model interactions of the G-quadruplex with cations in vivo.

Scanning tunneling microscopy shows that a layer of graphene can be grown on the hex-reconstructed Pt(100) surface and that the reconstruction is preserved after growth. A continuous sheet of graphene can be grown across domain boundaries and step edges without loss of periodicity or change in direction. Density functional theory calculations on a simple model system support the observation that the graphene can have different rotation angles relative to the hex-reconstructed Pt surface. The graphene sheet direction can be changed by incorporating pentagon-heptagon defects giving rise to accommodation of edge dislocations. The defect formation energy and the induced buckling of the graphene have been characterized by DFT calculations.

Combined scanning tunnelling microscopy measurements and density functional theory calculations reveal a method to induce linear structures of hydrogen adsorbates on graphite by covering the surface with a self-assembled molecular monolayer of cyanuric acid and exposing it to atomic hydrogen. The method can in principle be applied to obtain nanopatterned hydrogen structures on free standing graphene and graphene laid down on insulating substrates, hereby opening up for the possibility of substrate independent bandgap engineering of graphene.

The limitations of graphene as an effective corrosion-inhibiting coating on metal surfaces, here exemplified by the hex-reconstructed Pt(100) surface, are probed by scanning tunneling microscopy measurements and density functional theory calculations. While exposure of small molecules directly onto the Pt(100) surface will lift the reconstruction, a single graphene layer is observed to act as an effective coating, protecting the reactive surface from O(2) exposure and thus preserving the reconstruction underneath the graphene layer in O(2) pressures as high as 10(-4) mbar. A similar protective effect against CO is observed at CO pressures below 10(-6) mbar. However, at higher pressures CO is observed to intercalate under the graphene coating layer, thus lifting the reconstruction. The limitations of the coating effect are further tested by exposure to hot atomic hydrogen. While the coating can withstand these extreme conditions for a limited amount of time, after substantial exposure, the Pt(100) reconstruction is lifted. Annealing experiments and density functional theory calculations demonstrate that the basal plane of the graphene stays intact and point to a graphene-mediated mechanism for the H-induced lifting of the reconstruction.

Theoretical and experimental studies have revealed that the properties of graphene can be changed substantially by hydrogenation. Theoretical calculations show that fully hydrogenated graphene, referred to as graphane, is an insulator [1] and that hydrogen line structures can induce graphene nanoribbon – like band gaps in graphene [2]. Experimental investigations reveal a change of electronic properties of graphene upon hydrogenation [3-6]. The experiments also show that graphene hydrogenation is substrate dependent [6-9]. Here we report on the substrate dependence of hydrogen adsorbate structures on graphene on SiC, Ir(111), Pt(100) and graphite.

The possible role of neutral PAHs as catalysts for H2 formation in the interstellar medium is investigated by a combined experimental and density function theory study of the superhydrogenation of coronene (C24H12). The calculations suggest efficient hydrogenation of both edge and centre sites, along with competing abstraction reactions to form H2 in a series of catalytic cycles. Scanning tunneling microscopy and thermal desorption measurements have been used to provide direct evidence of the formation of superhydrogenated coronene as a result of exposure to D atoms. Lower limit estimates for the cross-sections of 1.8 × 10-17, 5.5 × 10-18 and 1.1 × 10-18 cm2 for the formation of singly, doubly and triply hydrogenated coronene are derived. The results suggest that superhydrogenated PAHs may play an important role in H2 formation in the ISM.

Xanthine molecule is an intermediate in nucleic acid degradation from the deamination of guanine and is also a compound present in the ancient solar system that is found in high concentrations in extraterrestrial meteorites. The self-assembly of xanthine molecules on inorganic surfaces is therefore of interest for the study of biochemical processes, and it may also be relevant to the fundamental understanding of prebiotic biosynthesis. Using a combination of high-resolution scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, two new homochiral xanthine structures have been found on Au(111) under ultrahigh vacuum conditions. Xanthine molecules are found to be self-assembled into two extended homochiral networks tiled by two types of di-pentamer units and stabilized by intermolecular double hydrogen bonding. Our findings indicate that the deamination of guanine into xanthine leads to a very different base pairing potential and the chemical properties of the base which may be of relevance to the function of the cell and potential development of human diseases. Moreover, the adsorption of xanthine molecules on inorganic surfaces leading to homochiral assemblies may be of interest for the fundamental understanding of the emerged chirality at early stages of life.

Violet Lander (C(108)H(104)) is a large organic molecule that when deposited on Cu(110) surface exhibits lock-and-key like behavior [Otero et al., Nature Mater. 3, 779 (2004)]. In this work, we report a detailed fully atomistic molecular mechanics and molecular dynamics study of this phenomenon. Our results show that it has its physical basis on the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of the matching between molecule and surface dimensions. This information could be used to find new molecules capable of displaying lock-and-key behavior with new potential applications in nanotechnology.

Supramolecular self-assembly on surfaces, guided by hydrogen bonding interactions, has been widely studied, most often involving planar compounds confined directly onto surfaces in a planar two-dimensional (2-D) geometry and equipped with structurally rigid chemical functionalities to direct the self-assembly. In contrast, so-called molecular Landers are a class of compounds that exhibit a pronounced three-dimensional (3-D) structure once adsorbed on surfaces, arising from a molecular backboard equipped with bulky groups which act as spacer legs. Here we demonstrate the first examples of extended, hydrogen-bonded surface architectures formed from molecular Landers. Using high-resolution scanning tunnelling microscopy (STM) under well controlled ultrahigh vacuum conditions we characterize both one-dimensional (1-D) chains as well as five distinct long-range ordered 2-D supramolecular networks formed on a Au(111) surface from a specially designed Lander molecule equipped with dual diamino-triazine (DAT) functional moieties, enabling complementary NH...N hydrogen bonding. Most interestingly, comparison of experimental results to STM image calculations and molecular mechanics structural modeling demonstrates that the observed molecular Lander-DAT structures can be rationalized through characteristic intermolecular hydrogen bonding coupling motifs which would not have been possible in purely planar 2-D surface assembly because they involve pronounced 3-D optimization of the bonding configurations. The described 1-D and 2-D patterns of Lander-DAT molecules may potentially be used as extended molecular molds for the nucleation and growth of complex metallic nanostructures.

In this study, through the choice of the well-known G-K biological coordination system, bioligand-alkali metal coordination has for the first time been brought onto an inert Au(111) surface. Using the interplay between high-resolution scanning tunneling microscopy and density functional theory calculations, we show that the mobile G molecules on Au(111) can effectively coordinate with the K atoms, resulting in a metallosupramolecular porous network that is stabilized by a delicate balance between hydrogen bonding and metal-organic coordination.

The involvement of surfaces in the origin of the first genetic molecules on Earth has long been suggested. Prior to the emergence of nucleic acid polymerases in the prebiotic soup, the self-assembly of primitive nucleobase building blocks may have relied on surface-mediated recognition events which catalyzed the formation of a covalent backbone in prototype oligonucleotides that subsequently may have functioned as templates in a primitive copying mechanism. This initial replication process may have been catalyzed by surfaces or chemical substances in solution—including RNA itself, as postulated in the RNA world hypothesis. Today, the role and the relative importance of the basic, fundamental driving forces for nucleic acid replication such as base pairing, base stacking, and steric effects are still under intense debate. Watson–Crick hydrogen bonding has traditionally been thought to be a prerequisite for high-fidelity DNA replication. However, recent studies on nucleobase analogues with the same size and shape as the natural ones but without relevant hydrogen-bonding groups have revealed that these analogues can recognize each other with high fidelity when incorporated into DNA sequences in vivo. Watson–Crick hydrogen bonding thus seems not to be a requisite for the selectivity of base pairing in DNA replication. However, in the absence of polymerases in the prebiotic soup, Watson– Crick hydrogen bonding may have played a more crucial role in the molecular recognition between the nucleobase building blocks at surfaces and for further polymerization. In support of this postulation, molecular recognition between complementary bases, most likely driven by hydrogen bonding alone, has already been observed both at the liquid/solid (HOPG) interface and on the noble Au(111) surface under extreme ultrahigh vacuum (UHV) conditions. These previous experiments were, however, conducted with nucleobases alone, and hence did not take the presence of deoxyribose into account. It is therefore of utmost importance to explore the role that Watson–Crick hydrogen bonding plays at surfaces in chemical structures that mimic nucleotides so as to address the fundamental question of how the polymerization of nucleotides may have started in the prebiotic soup in the absence of enzymes. The development of the scanning tunneling microscopy (STM) technique has advanced our understanding of supramolecular self-assembly systems on surfaces and has allowed intermolecular interactions to be explored at the submolecular scale. Herein we show by using a combination of high-resolution STM imaging and density functional theory (DFT) that sequential co-deposition of N-aryl-modified nucleobases cytosine (C) and guanine (G) onto the Au(111) surface under UHV conditions results in the formation of highly ordered supramolecular porous networks, where Watson–Crick hydrogen bonding between chemically modified C and G molecules plays the primary role in their stabilization. As the N-arylation of the nucleobases has been performed on the nitrogen atom normally attached to the sugar moiety in DNA or RNA (Scheme 1), these N-aryl-modified nucleobases thus represent two-dimensional (2D) structural mimics of naturally occurring nucleotides. The current results outline a new route for directing the self-assembly of nucleobase-derived nanostructures at the surface. Furthermore, the observed [*] Prof. W. Xu, Dr. M. F. Jacobsen, Dr. M. Yu, Prof. E. Laegsgaard, Prof. I. Stensgaard, Prof. T. R. Linderoth, Prof. J. Kjems, Prof. K. V. Gothelf, Prof. F. Besenbacher Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Department of Physics and Astronomy, Department of Chemistry, and Department of Molecular Biology, Aarhus University 8000 Aarhus C (Denmark) E-mail: fbe@inano.au.dk

Molecular Landers are a class of compounds containing an aromatic board as well as bulky side groups which upon adsorption of the molecule on a surface may lift the molecular board away from the substrate. Different molecular Landers have extensively been studied as model systems for nanomachines and the formation of molecular wires, as well as for their function as "molecular moulds", i.e., acting as templates by accommodating metal atoms underneath their aromatic board. Here, we investigate the adsorption of a novel Lander molecule 1,4-bis(4-(2,4-diaminotriazine)phenyl)-2,3,5,6-tetrakis(4-tert-butylphenyl)benzene (DAT, C64H68N10) on Cu(110) and Au(111) surfaces under ultrahigh vacuum (UHV) conditions. By means of scanning tunneling microscopy (STM) imaging and manipulation, we characterize the morphology and binding geometries of DAT molecules at terraces and step edges. On the Cu(110) surface, various contact configurations of individual DAT Landers were formed at the step edges in a controlled manner, steered by STM manipulation, including lateral translation, rotation, and pushing molecules to an upper terrace. The diffusion barrier of single DAT molecules on Au(111) is considerably smaller than on Cu(110). The DAT Lander is specially designed with diamino-triazine side groups making it suitable for future studies of molecular self-assembly by hydrogen-bonding interactions. The results presented here are an important guide to the choice of substrate for future studies using this compound.

Guanine molecules adsorbed on the Au(111) surface at room temperature are observed to form a heterochiral phase consisting of two homochiral G-quartet networks (see image, left). By annealing the sample at 400 K the R and L homochiral G-quartet networks are found to irreversibly transform to a heterochiral G-quartet network including both R and L G-quartets in an equal amount (see image, right).

From an interplay between scanning tunneling microscopy (STM) and ab initio density functional theory (DFT) we have identified and characterized two different self-assembled adenine (A) structures formed on the Au(111) surface. The STM observations reveal that both structures have a hexagonal geometry in which each molecule forms double hydrogen bonds with three nearest neighbors. One of the A structures, with four molecules in the primitive cell, has p2gg space group symmetry, while the other one, with two molecules in the cell, has p2 symmetry. The first structure is observed more frequently and is found to be the dominating structure after annealing. Experimental as well as theoretical findings indicate that the interaction of A molecules with the gold surface is rather weak and smooth across the surface. This enabled us to unequivocally characterize the observed structures, systematically predict all structural possibilities, based on all known A-A dimers, and provisionally optimize positions of the A molecules in the cell prior to full-scale DFT calculations. The theoretical method is a considerable improvement compared to the approach suggested previously by Kelly and Kantorovich [Surf. Sci. 589, 139 (2005)]. We propose that the less ordered p2gg symmetry structure is observed more frequently due to kinetic effects during island formation upon deposition at room temperature.

We present an interplay of high-resolution scanning tunneling microscopy imaging and the corresponding theoretical calculations based on elastic scattering quantum chemistry techniques of the adsorption of a gold-functionalized rosette assembly and its building blocks on a Au(111) surface with the goal of exploring how to fabricate functional 3-D molecular nanostructures on surfaces. The supramolecular rosette assembly stabilized by multiple hydrogen bonds has been sublimed onto the Au(111) surface under ultra-high vacuum conditions; the resulting surface nanostructures are distinctly different from those formed by the individual molecular building blocks of the rosette assembly, suggesting that the assembly itself can be transferred intact to the surface by in situ thermal sublimation. This unanticipated result will open up new perspectives for growth of complex 3-D supramolecular nanostructures at the vacuum-solid interface.

Binäre Mischungen der komplementären Nucleobasen Guanin (G) und Cytosin (C) auf einer Au(111)-Oberfläche bleiben durch die Bildung von Watson-Crick-Basenpaaren bis zur Desorptionstemperatur der Basen thermisch stabil. Dagegen segregieren binäre Mischungen der nichtkomplementären Basen Adenin (A) und Cytosin beim Erwärmen (siehe STM-Bilder mit DFT-Strukturen). Detailed facts of importance to specialist readers are published as "Supporting Information". Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.